So my problem was a quirk in FLStudio. They have a whole section under options for Midi Setting, but there is also just a separate selection under options that you have to make sure is checked for "enable MIDI out".
THAT SAID, my advice for anyone who is wanting to create MIDI files to control they gear is to NOT use your Sequencing program. Maybe some others do it better, but FLStudio is a little work and I found some challenges:
-No way I could find to put in PC messages to changes Presets during a song, and I read somewhere that PC changes are only available at the beginning of the MIDI file. While this may be true for MIDI files created in FLStudio, it is NOT the case in general. But I was having to work around this by controlling the individual loops on my loop switcher using CC's instead of the Presets I had created with PC's, and this was cumbersome. It also led to the realization that...
-You cannot fine tune the placement of CC's within FLStudio. You can turn the "Snap to" settings to NONE, but even at highest magnification of the measure, it will snap to a small increment that can leave you with gaps between CC's that are noticeable during play (Like if you are needing to turn off your mod effects while at the same time turning on overdrive for a chorus). Why not just put those CC's at the same point in time and trigger at once? Because....
-CC's are SERIAL commands. If you overlap them in time on your sequencers, things will not trigger. Even the most miniscule spacing in time and they work great. I spent a whole day learning this (synth guys chortle in the background). With the sequencer I tried setting it up with a running automation bar through the song that would alternate between the values for ON and OFF of a command. Quickly learned that you need a small slope when changing values or screwy things happened. Later learned it was best to create separate ON and OFF automations and put only a single DOT of data in the automation, and place it where needed. Still, I could not get the commands close enough to make changes of multiple pedals simultaneously work well, because the smallest space between commands was just too much. Soooooo....
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Again, synth guys roll their eyes in the backgraound and say "well DUH!!!"
So I switched to MidiEditor. I just thought there had to be some program for editing .Mid files, searched and there it was. I find it mildly clunky to use, but you can figure it out easily enough. With this you can either edit .Mid files you have made, or just create new ones. which is what I am doing for each song. Here are some highlights and tips:
1) This program allows you to place CC's and PC's on your timeline easily, just have to select parameters. For PC's you just select the program # and your MIDI channel (they number 0-15, not 1-16, so make the adjustment). For CC's you select the CC, the value you want, and the MIDI channel. Keep in mind that these commands CANNOT OVERLAP in time. You MUST have some space between commands, whether PC, CC, or Combos of the two. The overlap can be miniscule, and in the settings window for the command, they show you what "tick" in time you have placed the commands. If you have 2 commands you want performed simultaneously, just manually change the "tick" by a value of 1, and you are set. You could also nudge the little bar for the command, but you can get it closer by manually changing the value. Note the BARS on the timeline that represent your commands may overlap visually, as long as the "tick" in time where they start does not overlap.
2) Of course, you can also trigger notes in a synth with this program. I was mostly interested in commands.
3) You must also click on the TEMPO bar at the start of the timeline and enter the song tempo that you are trying to line up with.
4) For some reason that I cannot figure, the .Mid file does not line up as well with the songs when created in MidiEditor as they did when created in FLStudio. My work-around, which is easy enough, is to SELECT ALL when done and tweak the commands by sliding them a little to the right on the timeline. As I type this, I am thinking that maybe the issue is that the FLStudio files had a START command attached, and the ones I have created in MIDIEditor do not, and rely on the START Command that Bandhelper initiates, which may come briefly before the song autoplays in Bandhelper. I will investigate this theory further today.
5) OH....if you are creating a NEW file, you will be frustrated because MidiEditor only gives you 10 measures to work with. You have to go into TOOLS dropdown and there is a section SET FILE DURATION. I set it for 300000 which is more than enough for most songs, but you can input any value.
So I am not using this to change presets on my loop switcher and also record, play and stop loops during a song. The looper management was my main goal and it works well. I do have my looper (Pigtronic Infinity) set for MIDISYNC function and Bandhelper provides the Midiclock.
A quirk I found between using FLStudio and MidiEditor as far as running the looper: in FLStudio I could just place the Looper Rec/Play and Stop commands right at the start of the measure and it works fine. With the MidiEditor, I was having issues where the Stop and Play commands were not working right. The Play would trigger and show the loop queued up to play, and play at the next measure. When you have MidiSync enabled on the Infinity Looper, they suggest you trigger the loop JUST AHEAD of when you want it to ensure the loop plays or stops at the right time, because it quantizes the loop. Why this was not an issue in FLStudio files, I am unsure...maybe due to the START command theory I suggested. On my Infinity Looper I have it set to AUTO ZERO RECORD, which basically, as I understand it, retimes the Midiclock to your first loop record (the midiclock signal from Bandhelper obviously remains the same, but Infinity Looper recalibrates to respond consistently 3 milliseconds off the Midiclock beat, for example. Anyway, so the simple solution was to bump all looper commands AFTER the first record command back a little in time, and now they trigger fine.